Sequence and intramolecular distance scoring analyses of microbial rhodopsins [version 2; referees: 2 approved]

• Main Authors: Miki Asano, Shunta Ide, Atsushi Kamata, Kiyohiro Takahasi, Tetsuji Okada
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2016-04-01
• Series: F1000Research
• Subjects: Bioinformatics; Protein Chemistry & Proteomics
• Online Access: http://f1000research.com/articles/5-165/v2

Recent accumulation of sequence and structural data, in conjunction with systematical classification into a set of families, has significantly advanced our understanding of diverse and specific protein functions. Analysis and interpretation of protein family data requires comprehensive sequence and structural alignments. Here, we present a simple scheme for analyzing a set of experimental structures of a given protein or family of proteins, using microbial rhodopsins as an example. For a data set comprised of around a dozen highly similar structures to each other (overall pairwise root-mean-squared deviation < 2.3 Å), intramolecular distance scoring analysis yielded valuable information with respect to structural properties, such as differences in the relative variability of transmembrane helices. Furthermore, a comparison with recent results for G protein-coupled receptors demonstrates how the results of the present analysis can be interpreted and effectively utilized for structural characterization of diverse protein families in general.